Can you compare the current VirtualHost config files to one from before you deleted that cert.
Does each site have the correct DocumentRoot folder? I know we see the home page but none of the subfolder pages exist.
Does the output of this look right to you?
ls -l /var/www/html/keto-programs.com/public_html
It should have the subfolders for your other pages
And, when you say "I deleted a virtual host with a website"
How did you delete it? Was it some sort of admin system that somehow affected your other sites?